[Biopython] Normalizing paired distance in Treeconstruction
Jordan Willis
jwillis0720 at gmail.com
Wed Oct 14 05:24:26 UTC 2015
Hi,
I have a question about the pairwise distance calculation in the DistanceCalculator under Phylo.TreeConstruction.
It pertains to the normalization.
Line 456.
return 1 - (score * 1.0 / max_score)
I understand that the goal here is to have a distance between 0 and 1. But couldn’t this be greater than 1 if say score was negative as is allowed in PAM and BLOSUM lookup matrices. Perhaps the entire distance matrix should be computed, then a minimum and maximum derived, and then normalized between 0 and 1 rather than do it on a pairwise basis. What do you think?
Jordan
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20151013/25c4a685/attachment.html>
More information about the Biopython
mailing list